[phenixbb] installing phenix on Fedora core 10

amadrona at uci.edu amadrona at uci.edu
Thu Aug 5 11:21:41 PDT 2010

>> Thanks,
I run the jobs in the comand line in the background using & after the
command.  For some reason reason phenix is the only program that still
displays even with & which I don't understand.
I will try entering "screen_output &"


Thank you.  I can't believe how easy that was.  My phenix.maps problem
>> is
>> solved.  It works as it should.  I was also having a problem in not
>> getting a pdb or mtz to export for wxc optimization (see below) so I
>> will
>> rerun this tonight and hopefully everything will go smoothly.  Thanks
>> again.
> ...
>>   File "/usr/local/phenix-1.6-289/cctbx_project/libtbx/utils.py", line
>> 666, in write
>>     file_object.write(str)
>> IOError: [Errno 5] Input/output error
> This probably means you lost your "stdout" or "stderr", e.g. by
> starting phenix.refine and then closing the terminal window or GUI. In
> case you run from the command line and anticipate your terminal window
> may not survive the entire run, it is best done like this:
>   phenix.refine some.pdb some.mtz some.params >& screen_output &
> If it happens when running from the GUI Nat may have more to say.
> Ralf
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